MAPPING CHARACTERS IN TNT

TNT makes it possible to map synapomorphies onto your tree. This is useful for determining your new
species autapomorphies (diagnostic characters) and synapomorphies for clades within your ingroup.
Note that you need to have a tree already in TNTs memory or mapping options will not be available.
Mapping characters is done by going to Optimize > Synapomorphies > Map Synapomorphies.
This brings up a window where you can select onto which trees you want the synapomorphies mapped.
You can tell it only to map onto selected trees, which will bring up a new window allowing you to include
or exclude trees from mapping. Remember, that TNT starts numbering at 0, so the character numbers
may not necessarily correspond to the character numbers in another program (e.g., Mesquite, where
each will be off by one). Also remember that as analysis software, TNT doesnt care about character
polarity. You will need to wait until mapping the character history in Mesquite to figure out the states
for your synapomorphies and autapomorphies.
MAPPING CHARACTERS IN MESQUITE
This is one of the most useful functions of Mesquite. It allows you to trace the characters you used in
your analysis onto your tree. It helps you interpret where character-state changes may have occurred
and also makes it very clear if certain characteristics have evolved more than once according to your
cladogram. It lets you see the synapomorphies and autapomorphies of each clade and taxon (This is
something you will definitely want to know for your paper!).
Again, there are many different ways you can trace characters onto your tree and a lot of different
parameters you can tweak. Generally, you will be interested in the morphological changes but will not
need to know the molecular changes to diagnose the new species or other taxa. Even if your preferred
tree is derived from molecular data, you must trace the morphological character state changes on to it,
because this will be used in the diagnosis of the new species. To do this onto the molecular tree open
the morphological data file first, and then open a molecular tree file. Then, map the morphological
character-state changes onto this tree as outlined above.
To trace the characters onto your tree, go to Analysis > Trace Character History. Youll want to use
Stored Characters. If you want to reconstruct the ancestral states for each internal node using
parsimony, select Parsimony Ancestral States. The character history displayed can be reconstructed
using observed states in terminal taxa (Reconstruct Ancestral States) or can be a simulated history
(Simulate Ancestral States). Youll want to go with Reconstruct Ancestral States.
Along with colouring the trees branches to illustrate character states, you should see a tree legend pop
up (usually in the bottom left corner of the tree window). This legend gives you detailed character
information and allows you to navigate among all of the possible characters from your matrix.
As a final option, you may want to know which ancestral nodes are equivocal with respect to their
reconstructed character states. You can use different shading to denote this by going to Trace > Use
Gray for Equivocal.
FIT STATISTICS IN MESQUITE
There are a few other things you may want to calculate, including consistency and retention. This is
useful because its something TNT does not do without adding in your own block of code to the
program. These (and the tree length, etc.) can be calculated by going to Analysis > Values for Current
Tree Again, youll be using Stored Matrices from which to calculate these values. Once youve done
that, Mesquite opens up a legend in the tree window with the values youve specified. Repeating the
process will bring up a brand new legend over the existing one. You can tell the program to add new
values into the same legend by going to Legend > Show and selecting values from the menu provided.
If you want tree info without having a legend within the tree window itself (the legend will show up
when you save the tree as a PDF). If not, you can create a new tree info panel by clicking on in the lower
left hand corner of the tree window. In the info panel, you can click on the + sign next to Values to add
in any new values you would like.